Variant report

Variant	rs2622695
Chromosome Location	chr3:137844645-137844646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1564496	0.91[EUR][1000 genomes]
rs1600697	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2170309	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2219936	0.86[CEU][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2246945	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2251550	0.85[EUR][1000 genomes]
rs2346747	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs2622694	0.86[CEU][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2622696	0.88[EUR][1000 genomes]
rs2622697	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2622699	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2622700	0.81[CEU][hapmap]
rs2622714	0.83[JPT][hapmap]
rs2622733	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs2622734	0.81[CEU][hapmap]
rs2622735	0.81[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2622736	0.81[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2622737	0.81[CEU][hapmap]
rs2622742	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2622743	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2622744	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2724687	0.95[CEU][hapmap]
rs2724690	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2724691	0.86[CEU][hapmap];0.89[CHD][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2724692	0.86[CEU][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2724711	0.88[EUR][1000 genomes]
rs2724712	0.81[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2724726	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2724727	0.81[CEU][hapmap]
rs367439	0.81[JPT][hapmap]
rs3732839	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs405602	0.80[JPT][hapmap]
rs4678403	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs608594	0.81[CEU][hapmap]
rs7613558	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7632402	0.87[EUR][1000 genomes]
rs774803	0.81[CEU][hapmap]
rs774807	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs774808	0.81[CEU][hapmap]
rs774810	0.81[CEU][hapmap]
rs774813	0.81[CEU][hapmap]
rs774814	0.81[CEU][hapmap]
rs811811	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs9857908	0.83[GIH][hapmap]
rs9874211	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2622695	A4GNT	cis	lung	GTEx
rs2622695	A4GNT	cis	Esophagus Mucosa	GTEx
rs2622695	A4GNT	cis	Adipose Subcutaneous	GTEx
rs2622695	A4GNT	cis	Thyroid	GTEx
rs2622695	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2622695	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs2622695	A4GNT	cis	Artery Tibial	GTEx
rs2622695	A4GNT	cis	Nerve Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137842600-137845800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:137842800-137845400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr3:137843000-137845000	Enhancers	Fetal Muscle Leg	muscle
4	chr3:137843000-137845200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr3:137843200-137845000	Enhancers	Primary B cells from cord blood	blood
6	chr3:137843200-137845000	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr3:137843400-137845000	Enhancers	Brain Hippocampus Middle	brain
8	chr3:137843600-137845000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:137843600-137845000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:137843600-137845000	Enhancers	Fetal Stomach	stomach
11	chr3:137843600-137845000	Enhancers	Pancreas	Pancrea
12	chr3:137843600-137845000	Enhancers	HMEC	breast
13	chr3:137843600-137845000	Enhancers	NH-A	brain
14	chr3:137843600-137845000	Enhancers	NHLF	lung
15	chr3:137843600-137845200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:137843600-137845200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:137843600-137845200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:137843600-137845400	Enhancers	Fetal Heart	heart
19	chr3:137843800-137845000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:137843800-137851800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:137844200-137844800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:137844200-137844800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:137844200-137844800	Flanking Active TSS	Osteobl	bone
24	chr3:137844200-137845000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:137844200-137845000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:137844200-137845000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:137844200-137845000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:137844200-137845000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:137844200-137845000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:137844200-137845000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr3:137844200-137845000	Enhancers	Right Ventricle	heart
32	chr3:137844200-137845000	Enhancers	NHDF-Ad	bronchial
33	chr3:137844200-137845200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:137844200-137845200	Enhancers	A549	lung
35	chr3:137844400-137844800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:137844400-137844800	Enhancers	Stomach Mucosa	stomach
37	chr3:137844400-137844800	Flanking Active TSS	HSMM	muscle
38	chr3:137844400-137844800	Flanking Active TSS	HSMMtube	muscle
39	chr3:137844400-137845000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:137844400-137845000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:137844400-137845000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:137844400-137845000	Enhancers	Colon Smooth Muscle	Colon
43	chr3:137844600-137844800	Enhancers	Placenta	Placenta
44	chr3:137844600-137844800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:137844600-137845200	Enhancers	Adipose Nuclei	Adipose
46	chr3:137844600-137845200	Enhancers	Left Ventricle	heart

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